Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19

J Cheng, J Zhang, Z Wu, X Sun - Briefings in bioinformatics, 2021 - academic.oup.com
Inferring how gene expression in a cell is influenced by cellular microenvironment is of great
importance yet challenging. In this study, we present a single-cell RNA-sequencing data …

The Role of BRCA1/2-Mutated Tumor Microenvironment in Breast Cancer

S Miklikova, L Trnkova, J Plava, M Bohac, M Kuniakova… - Cancers, 2021 - mdpi.com
Simple Summary The link between BRCA1/2 mutations and high susceptibility to breast
cancer development has been well-established for years. However, the potential impact of …

Patient-specific multi-omics models and the application in personalized combination therapy

A John, B Qin, KR Kalari, L Wang, J Yu - Future Oncology, 2020 - Taylor & Francis
The rapid advancement of high-throughput technologies and sharp decrease in cost have
opened up the possibility to generate large amount of multi-omics data on an individual …

MeSHHeading2vec: a new method for representing MeSH headings as vectors based on graph embedding algorithm

ZH Guo, ZH You, DS Huang, HC Yi… - Briefings in …, 2021 - academic.oup.com
Abstract Effectively representing Medical Subject Headings (MeSH) headings (terms) such
as disease and drug as discriminative vectors could greatly improve the performance of …

A computational study of potential miRNA-disease association inference based on ensemble learning and kernel ridge regression

LH Peng, LQ Zhou, X Chen, X Piao - Frontiers in bioengineering and …, 2020 - frontiersin.org
As increasing experimental studies have shown that microRNAs (miRNAs) are closely
related to multiple biological processes and the prevention, diagnosis and treatment of …

Comparative analysis of protein-protein interaction networks in metastatic breast cancer

H Hozhabri, RS Ghasemi Dehkohneh, SM Razavi… - PloS one, 2022 - journals.plos.org
Metastatic lesions leading causes of the majority of deaths in patients with the breast cancer.
The present study aimed to provide a comprehensive analysis of the differentially expressed …

Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response

M Pagadala, TJ Sears, VH Wu, E Pérez-Guijarro… - Nature …, 2023 - nature.com
With the continued promise of immunotherapy for treating cancer, understanding how host
genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring …

Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods

T Gui, C Yao, B Jia, K Shen - PLoS One, 2021 - journals.plos.org
Background Though considerable efforts have been made to improve the treatment of
epithelial ovarian cancer (EOC), the prognosis of patients has remained poor. Identifying …

Plasma exosome-derived microRNAs expression profiling and bioinformatics analysis under cross-talk between increased low-density lipoprotein cholesterol level …

C Liu, Y Lai, S Ying, J Zhan, Y Shen - Journal of Translational Medicine, 2020 - Springer
Background Exosome-derived microRNAs (exo-miRs) as messengers play important roles,
in the cross-talk between genetic [ATP-sensitive potassium channels (KATP) genetic variant …

Breast Tumor Metastasis and Its Microenvironment: It Takes Both Seed and Soil to Grow a Tumor and Target It for Treatment

S Bonni, DN Brindley, MD Chamberlain… - Cancers, 2024 - mdpi.com
Simple Summary Metastasis is one of the biggest challenges in treating breast cancer.
Breast tumors grow in different areas such as the brain, lungs and bone and have distinct …